Literature DB >> 20372975

SAMPL2 and continuum modeling.

Anthony Nicholls1, Stanislaw Wlodek, J Andrew Grant.   

Abstract

An account is given of our contributions to the SAMPL2 challenge for vacuum-water transfer energies. These contributions include different charge sets and radii used with Poisson-Boltzmann continuum theory applied to a single low-energy conformation. A rationale for this approach is given, including a summary of what we have learnt over previous SAMPL events. The results strongly suggest the need for new and repeated experimental measurements, both to clarify what appears to be experimental discrepancies in older measurements and to advance the field in a statistically sound manner.

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Year:  2010        PMID: 20372975     DOI: 10.1007/s10822-010-9334-8

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  11 in total

1.  The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.

Authors:  Emilio Gallicchio; Linda Yu Zhang; Ronald M Levy
Journal:  J Comput Chem       Date:  2002-04-15       Impact factor: 3.376

2.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors:  Araz Jakalian; David B Jack; Christopher I Bayly
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

3.  The SAMPL2 blind prediction challenge: introduction and overview.

Authors:  Matthew T Geballe; A Geoffrey Skillman; Anthony Nicholls; J Peter Guthrie; Peter J Taylor
Journal:  J Comput Aided Mol Des       Date:  2010-05-09       Impact factor: 3.686

4.  Analysis of SM8 and Zap TK calculations and their geometric sensitivity.

Authors:  Benjamin A Ellingson; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2010-04-30       Impact factor: 3.686

5.  A density functional that accounts for medium-range correlation energies in organic chemistry.

Authors:  Yan Zhao; Donald G Truhlar
Journal:  Org Lett       Date:  2006-12-07       Impact factor: 6.005

6.  Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

Authors:  Anthony Nicholls; David L Mobley; J Peter Guthrie; John D Chodera; Christopher I Bayly; Matthew D Cooper; Vijay S Pande
Journal:  J Med Chem       Date:  2008-01-24       Impact factor: 7.446

7.  Treating entropy and conformational changes in implicit solvent simulations of small molecules.

Authors:  David L Mobley; Ken A Dill; John D Chodera
Journal:  J Phys Chem B       Date:  2008-01-03       Impact factor: 2.991

8.  On the calculation of electrostatic interactions in proteins.

Authors:  M K Gilson; A Rashin; R Fine; B Honig
Journal:  J Mol Biol       Date:  1985-08-05       Impact factor: 5.469

9.  Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects.

Authors:  K A Sharp; A Nicholls; R F Fine; B Honig
Journal:  Science       Date:  1991-04-05       Impact factor: 47.728

10.  SM6:  A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters.

Authors:  Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2005-11       Impact factor: 6.006

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  10 in total

1.  The SAMPL2 blind prediction challenge: introduction and overview.

Authors:  Matthew T Geballe; A Geoffrey Skillman; Anthony Nicholls; J Peter Guthrie; Peter J Taylor
Journal:  J Comput Aided Mol Des       Date:  2010-05-09       Impact factor: 3.686

2.  Analysis of SM8 and Zap TK calculations and their geometric sensitivity.

Authors:  Benjamin A Ellingson; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2010-04-30       Impact factor: 3.686

3.  Efficient calculation of SAMPL4 hydration free energies using OMEGA, SZYBKI, QUACPAC, and Zap TK.

Authors:  Benjamin A Ellingson; Matthew T Geballe; Stanislaw Wlodek; Christopher I Bayly; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2014-03-16       Impact factor: 3.686

4.  Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding.

Authors:  E V Katkova; A V Onufriev; B Aguilar; V B Sulimov
Journal:  J Mol Graph Model       Date:  2016-12-21       Impact factor: 2.518

Review 5.  Blind prediction of solvation free energies from the SAMPL4 challenge.

Authors:  David L Mobley; Karisa L Wymer; Nathan M Lim; J Peter Guthrie
Journal:  J Comput Aided Mol Des       Date:  2014-03-11       Impact factor: 3.686

6.  Assessment of tautomer distribution using the condensed reaction graph approach.

Authors:  T R Gimadiev; T I Madzhidov; R I Nugmanov; I I Baskin; I S Antipin; A Varnek
Journal:  J Comput Aided Mol Des       Date:  2018-01-29       Impact factor: 3.686

7.  SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model.

Authors:  Caitlin C Bannan; David L Mobley; A Geoffrey Skillman
Journal:  J Comput Aided Mol Des       Date:  2018-10-15       Impact factor: 3.686

8.  Parameterization of a geometric flow implicit solvation model.

Authors:  Dennis G Thomas; Jaehun Chun; Zhan Chen; Guowei Wei; Nathan A Baker
Journal:  J Comput Chem       Date:  2012-12-05       Impact factor: 3.376

9.  Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.

Authors:  Luke J Gosink; Christopher C Overall; Sarah M Reehl; Paul D Whitney; David L Mobley; Nathan A Baker
Journal:  J Phys Chem B       Date:  2017-01-04       Impact factor: 2.991

10.  Detection of tautomer proportions of dimedone in solution: a new approach based on theoretical and FT-IR viewpoint.

Authors:  Sedat Karabulut; Hilmi Namli; Jerzy Leszczynski
Journal:  J Comput Aided Mol Des       Date:  2013-08-07       Impact factor: 3.686

  10 in total

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